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Analysis pipelines from Oxford Nanopore Technologies' Research Division
koszullab / hicstuff
Forked from baudrly/hicstuffSimple library/pipeline to generate and handle Hi-C data.
Various scripts and recipes for working with nanopore data
Command-line utility to color objects of a KEGG pathway with arbitrary colors
This repository contains the source code of JUDI, a workflow management system for developing complex bioinformatics software with many parameter settings. Bioinformatics pipeline: Just Do It!
Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
Unzip assembly graphs with Hi-C data and/or long reads.
Miscellaneous scripts for applications of PacBio systems
CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies
This repository is deprecated, please use the link to the right.
Scripts for homology and orthology assessment from genomic sequences.
(check out instaGRAAL for a faster, updated program!) This program is from Marie-Nelly et al., Nature Communications, 2014 (High-quality genome assembly using chromosomal contact data), also Marie-…
a simulator of long read sequencing in pacbio and oxford nanopore
Correction of palindromes in long reads from PacBio and Nanopore
ZGA prokaryotic genome assembly and annotation pipeline
This tool is for users to upgrade their metagenomics assemblies using long reads. This includes fixing mis-assemblies and scaffolding/gap-filling.
Workflow for detecting genome-wide horizontal gene transfers
Novo&Stitch is a genome assembly reconciliation tool based on optical map.
Hybrid Error Correction of Long Reads using Iterative Learning
Pipeline to phase a genome into two homeologous subgenomes. Parental genomes are required.
Long-read validation of BEDPE structural variation
Marker Gene Selection Tool For Spatial Transcriptomics